March 27, 2010

Natural selection behind population differentiation

A very important finding of the paper is that the correlation between recombination rate and genetic differentiation (as measured by Fst) is stronger between Africans and non-Africans, and weaker between Europeans and Chinese. To simplify, we can say that Eurasians and Africans have diverged from each other to a great part because of selection (in either Eurasians, or Africans, or both) that took them away (genetically) from their common ancestor. On the other hand, differentiation between Europeans and Chinese is to a greater extent neutral, i.e., the result of demographic separation, rather than independent processes of selection.

PLoS Genetics doi:10.1371/journal.pgen.1000886

Human Population Differentiation Is Strongly Correlated with Local Recombination Rate

Alon Keinan et al.

Abstract

Allele frequency differences across populations can provide valuable information both for studying population structure and for identifying loci that have been targets of natural selection. Here, we examine the relationship between recombination rate and population differentiation in humans by analyzing two uniformly-ascertained, whole-genome data sets. We find that population differentiation as assessed by inter-continental FSTshows negative correlation with recombination rate, with FST reduced by 10% in the tenth of the genome with the highest recombination rate compared with the tenth of the genome with the lowest recombination rate (P≪10−12). This pattern cannot be explained by the mutagenic properties of recombination and instead must reflect the impact of selection in the last 100,000 years since human continental populations split. The correlation between recombination rate andFST has a qualitatively different relationship for FST between African and non-African populations and for FST between European and East Asian populations, suggesting varying levels or types of selection in different epochs of human history.

The article is important as it constitutes another reminder that such genetic attributes of African populations as high intragroup diversity may stem not from greater absolute age of African populations over non-African populations but rather from other factors such as selection. Although the authors imply that their findings are compatible with the recent out of African model of human dispersals, their data suggests that it's not as certain as some scholars would like it to be.

What Average Joe wrote doesn't seem to have any bearing on the directionality of migrations, no? As humans expanded from East Asia westward, their movement to Europe was just "smoother" than their movement into Africa. Had they expanded from Africa and ended up in Southeast Asia, then their subsequent migration to Europe would have exposed them to much greater effects of selection.

Regardless of what population was affected by selection the most, what is remarkable about this paper is that the most salient feature of human genetic diversity, namely the "split" between African and non-African populations can be explained as an artifact of selection.

Being primates, human evolved to live in the hot, humid environment of Africa. When they left Africa for Ice Age Eurasia, they were moving into a very different environment than the one their ancestors evolved in and so would have experienced greater selection than the ones who stayed in tropical Africa. Also Africans tended to live in small tribal communities so your argument doesn't hold water.

Not necessarily. Larger populations usually have more variation, but selection on that variation will only work if the population is not actually expanding in numbers. If numbers are expanding the variation will be maintained. For the postulated ex-African migration selection could be quite severe as small subsets of the main group moved into different regions.

I thought that's what the paper says: "In view of the large effective population size in recent human history since each of these pairs of populations have split, these observations support the possibility that the different patterns observed between different pairs of populations are due to natural selection operating more efficiently in the context of larger population sizes."

Someone on Razib's site left a similar comment: "In larger populations, natural selection is more effective (there are fewer effectively neutral mutations — those with -1 less than Ns less than 1), which will lead to more fixations of slightly beneficial mutations and loss of slightly deleterious mutations due to selection. The background selection you’re talking about here (i.e., what’s occurring in small populations) won’t leave as large of a signature around the deleterious allele because it’s an older variant, and recombination would have decreased LD around that site."

"For the postulated ex-African migration selection could be quite severe as small subsets of the main group moved into different regions."

We have Hofmeyer skull at 36,000 YBP in South Africa that clusters with Eurasian populations and not with Bushmen or other African populations. It's a pretty direct evidence that African populations were affected by a strong "force," whether selective or demographic.

Average Joe:

"Also Africans tended to live in small tribal communities..."

Those small tribal populations are much more prevalent outside of Africa, namely in America, Papua New Guinea and parts of Asia. Hence, it's there and not in Africa, we have the largest number of linguistic isolates.

Those small tribal populations are much more prevalent outside of Africa, namely in America, Papua New Guinea and parts of Asia. Hence, it's there and not in Africa, we have the largest number of linguistic isolates

But Europe and much of Asia had towns and cities which would have been larger than the African population centers.

I can see now why natural selection could be more effective in a larger population; if limited resources prevented the population from increasing selection pressure on the greater number of beneficial mutations available would lead to their rapid increase. But we would still require some level of inbreeding somewhere within that population to allow advantageous recessive genes to form a phenotype. Once an advantageous gene is introduced as a phenotype into the wider population change could be rapid. So treating the whole human species as a single population we can see how evolution could have been rapid at times during our prehistory.

"So treating the whole human species as a single population we can see how evolution could have been rapid at times during our prehistory."

So, a single origin with rapid "replacement" scenario is more compatible with the cumulative increase of diversity in growing daughter populations, than with bottlenecks' scenario whereby an expansion from a homeland has led to the progressive loss of diversity in daughter populations and a steady increase in diversity in the parent population.

"So, a single origin with rapid 'replacement' scenario is more compatible with the cumulative increase of diversity in growing daughter populations"

'Single origin' does imply a small population, so its evolution should be slow. The 'daughter' populations would originally have been even smaller, so even slower evolution. The fact that diversity seems to be quite rapid implies that the 'single origin' theory is wrong.

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